1VA1 Transcription date Feb 07, 2004
title Solution Structure Of Transcription Factor Sp1 Dna Binding D (Zinc Finger 1)
authors S.Oka, Y.Shiraishi, T.Yoshida, T.Ohkubo, Y.Sugiura, Y.Kobayashi
compound source
Molecule: Transcription Factor Sp1
Chain: A
Fragment: Zinc Finger 1
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sp1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pevsp1
methodSolution NMR
ligand ZN enzyme
Primary referenceNMR structure of transcription factor Sp1 DNA binding domain., Oka S, Shiraishi Y, Yoshida T, Ohkubo T, Sugiura Y, Kobayashi Y, Biochemistry 2004 Dec 28;43(51):16027-35. PMID:15609997
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (305 Kb) [Save to disk]
  • Biological Unit Coordinates (1va1.pdb1.gz) 10 Kb
  • LPC: Ligand-Protein Contacts for 1VA1
  • CSU: Contacts of Structural Units for 1VA1
  • Original NMR restraints for 1VA1 from PDB
  • Retrieve 1VA1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VA1 from S2C, [Save to disk]
    • View 1VA1 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1VA1
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VA1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u1va1, region A:1-128 [Jmol] [rasmolscript] [script source]
        - Domain d1a1va1, region A:190-325 [Jmol] [rasmolscript] [script source]
        - Domain d1f1va1, region A:4-147 [Jmol] [rasmolscript] [script source]
        - Domain d1n1va1, region A:413-634 [Jmol] [rasmolscript] [script source]
        - Domain d1s1va1, region A:430-539 [Jmol] [rasmolscript] [script source]
        - Domain d1h1va1, region A:5-146 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1va1_A] [1va1]
  • SWISS-PROT database: [P08047]
  • Domain organization of [SP1_HUMAN] by SWISSPFAM
  • Domain found in 1VA1: [ZnF_C2H2 ] by SMART
    • Other resources with information on 1VA1
  • Community annotation for 1VA1 at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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